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Yorodumi- PDB-6lyk: Crystal Structure of R1263A mutant of Formylglycinamidine Synthetase -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lyk | ||||||
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Title | Crystal Structure of R1263A mutant of Formylglycinamidine Synthetase | ||||||
Components | Phosphoribosylformylglycinamidine synthase | ||||||
Keywords | LIGASE / Formylglycinamidine Synthetase | ||||||
Function / homology | Function and homology information phosphoribosylformylglycinamidine synthase / phosphoribosylformylglycinamidine synthase activity / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / glutamine metabolic process / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Sharma, N. / Tanwar, A.S. / Anand, R. | ||||||
Funding support | India, 1items
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Citation | Journal: Acs Catalysis / Year: 2022 Title: Mechanism of Coordinated Gating and Signal Transduction in Purine Biosynthetic Enzyme Formylglycinamidine Synthetase. Authors: Sharma, N. / Singh, S. / Tanwar, A.S. / Mondal, J. / Anand, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lyk.cif.gz | 325.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lyk.ent.gz | 249.9 KB | Display | PDB format |
PDBx/mmJSON format | 6lyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lyk_validation.pdf.gz | 891 KB | Display | wwPDB validaton report |
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Full document | 6lyk_full_validation.pdf.gz | 912.8 KB | Display | |
Data in XML | 6lyk_validation.xml.gz | 64.9 KB | Display | |
Data in CIF | 6lyk_validation.cif.gz | 101.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/6lyk ftp://data.pdbj.org/pub/pdb/validation_reports/ly/6lyk | HTTPS FTP |
-Related structure data
Related structure data | 6lylC 6lymC 6lyoC 7dw7C 1t3tS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 142509.359 Da / Num. of mol.: 1 / Mutation: R1263A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: purL, STM2565 / Production host: Escherichia coli (E. coli) References: UniProt: P74881, phosphoribosylformylglycinamidine synthase |
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-Non-polymers , 8 types, 1530 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-IMD / | #4: Chemical | ChemComp-ADP / | #5: Chemical | ChemComp-GLN / | #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-GOL / #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2M Ammonium Sulphate |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. obs: 188832 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.959 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 1.7→1.79 Å / Num. unique obs: 29675 / Rrim(I) all: 0.596 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1T3T Resolution: 1.7→39.74 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.743 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.08 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 146.97 Å2 / Biso mean: 21.324 Å2 / Biso min: 8.34 Å2
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Refinement step | Cycle: final / Resolution: 1.7→39.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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